No, the Wuhan Virus Is Not a ‘Snake Flu’

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Sharing data during an outbreak is vital for public health. But it can also lead to sensational, and even spurious research, like a controversial new paper claiming people probably picked up a novel coronavirus from snakes.

One of the many mysteries behind the outbreak of a new respiratory tract-attacking virus that’s now infected nearly 650 and killed 18 people in China is where, exactly, it came from. The initial cluster of pneumonia-like cases showed up in the city of Wuhan mid-December, and most of those patients had some tie to a wet market there—a place where people sell both live and dead animals, including exotic species, from snugly-abutting stalls.

Though nothing has been confirmed, epidemiologists suspect that the novel coronavirus crossed over into humans somewhere inside the market, which has been shuttered since January 1. Tracking down the right viral culprit is paramount to preventing future inter-species spillover. In 2003, when SARS ripped through the same area of China, the outbreak was fully contained only when the civet cats, which had passed the virus along to humans, were removed from region’s markets.

A national task force of Chinese researchers working swiftly to isolate and sequence the virus shared a draft of its genome in a public database earlier this month. That enabled labs all over the world to design diagnostic tests to flag cases as they spread outside of China. So far, fewer than a dozen cases have been confirmed in other countries, including Japan, Korea, Singapore, Thailand, Vietnam, and the US. The release of genetic data has also spurred a flurry of new research findings in recent days, including one paper published by a team of Chinese researchers last night in the Journal of Medical Virology that claims to have used the viral sequence to find the most likely source of the emerging outbreak’s origin. Their theory: snakes.

Amplified by a press release and a widely-syndicated editorial written by three senior editors of the journal, you can guess what happened next. Stories about China’s “snake flu” began to spread through social media alongside official reports about new confirmed cases. There’s just one problem: Other researchers think it’s probably not true.

“It’s complete garbage,” says Edward Holmes, a zoologist at the University of Sydney’s Institute for Infectious Diseases and Biosecurity, who specializes in emerging RNA viruses, a class that includes coronaviruses like 2019-nCoV. Holmes, who also holds appointments at the Chinese CDC and Fudan University in Shanghai, is among a number of scientists in virology forums, science Slacks, and on Twitter pointing out what they deem major flaws in the paper and calling on the journal to have it retracted. “It’s great that viral sequence data is getting shared openly in real time,” says Holmes. “The downside is then you get people using that data to make conclusions they really shouldn’t. The result is just a really unhelpful distraction that smacks of opportunism.”

Preliminary analyses of the genetic data released by Chinese authorities suggest that 2019-nCoV is most closely related to a group of coronaviruses that typically infect bats. But for a variety of reasons—including that it’s winter and bats are hibernating—many scientists suspect that some other animal moved the virus from bats to humans.

The Chinese team, led by Wei Ji, a microbiologist at Peking University Health Science Center School of Basic Medical Sciences, set out to find the identity of this unknown intermediate host. One way is using genetic data to look at codons—triplets of DNA or RNA letters that are the instructions for making proteins. Every organism has its own bias for which codon it uses to make its proteins. Some viruses adapt to new hosts by adopting their codon bias. Wei’s team compared the codons preferred by 2019-nCoV to those preferred by a handful of potential hosts: humans, bats, chickens, hedgehogs, pangolins, and two species of snakes.

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